AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -icpxR_pyro_opreg_300.orf -g0.419 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0479_PH0480 31 PH0479: 277aa long hypothetical methyl-accepting chemotaxis protein, PH0480: 110aa long hypothetical protein #2 PH0481 263 280aa long hypothetical chemotaxis protein methyltransferase #3 PH1408 233 226aa long hypothetical protein #4 PH1409 250 721aa long hypothetical protein #5 PH1410 117 332aa long hypothetical dipeptide transport system permease protein dppB #6 PH1414 26 129aa long hypothetical protein #7 PH1415 93 343aa long hypothetical 5' nuclease Motif number 1 CTCCTTTATTTCCTTATCGAGGTCTTCAACG 1 9 0 TTCTATCAGT 0.748045 -23 GGAAGACTTATGAACTCTTCATTTTGCTCACTACC 2 15 1 TACCTTCTTT 0.702638 -249 TGTAAAAAAGTTTTCGTCTCTTCTTTTAATGAAGC 2 72 1 TTCTCTCTTT 0.977924 -192 GCCTAGTAGTTTTACATCTCCATTTTTGAAGTTTA 2 105 1 TTCTCTCATT 0.971446 -159 AATCCACCCCTCAACTTGGATTTTGTT 2 247 0 TCCCCTCATT 0.915668 -17 ATTTCATAGGCGTACATCTCTCTTTCCTCGAGGAT 3 39 0 CTCTCTCCTT 0.981274 -195 GCTTGTAATATATCCTCTTCCCCTTTCTATATGCC 3 158 0 TTCCTTCCTT 0.97951 -76 CAATAAGCCTTCTACCTCTCTCAGTCAGCTTGTAA 3 185 0 TTCTCTCCGT 0.981274 -49 TAATCTTTCTTCTCTCTTTTCTTTATTGC 5 5 1 CTCTCTCCTT 0.981274 -113 ATTTGCCCCTCCTTGTACATTCTTGT 5 102 0 TTCCCTCTGT 0.976513 -16 ATATCCTCTTCTTTTTTCAATTTTTG 6 2 1 TTCCTTCTTT 0.953272 -25 TGATGATGAACCTTCCCCTCACCTGAAAGGTGATG 7 41 1 CTCCCTCCTG 0.938898 -53 AGCCTACCGGTGTGCTCATCACCTTTCAGGTGAGG 7 57 0 TTCCATCCTT 0.970898 -37 * * * **** * ** Masking position 9 Map Score: 15.8486 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 336 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 TGAAGAGTTCATAAGTCTTCCTGGG 2 6 0 ATAAGTCTTC 0.924875 -258 CTATACAATGATAAACCTTCCTTAATAAAA 2 184 0 ATAAACCTTC 0.98382 -80 TCCCCTTTCTATATGCCTCCTTTATGAGGC 3 145 0 ATATGCCTCC 0.906342 -89 AAGATTTTCAATAAGCCTTCTACCTCTCTC 3 198 0 ATAAGCCTTC 0.992089 -36 CACCTCGCTAATAAGCTTTTCGATCTTGGT 4 189 0 ATAAGCTTTT 0.854895 -62 ATCTCTTTGGATAACCTTCCCTGGTGATGT 4 228 1 ATAACCTTCC 0.942294 -23 ATTGTTATAAACTTTCAGAGATATCA 7 7 1 ATAAACTTTC 0.968673 -87 AAGTCTGATGATGAACCTTCCCCTCACCTG 7 36 1 ATGAACCTTC 0.941693 -58 CGGTGTGCTCATCACCTTTCAGGTGAGGGG 7 55 0 ATCACCTTTC 0.898723 -39 ********** Masking position 8 Map Score: 9.71447 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 253 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 CTTTTTTACATATTTTAACGAAGGTCATAATT 2 50 0 TATTTTAGAA 0.962208 -214 TTTCGTCTCTTCTTTTAATGAAGCCTAGTAGT 2 83 1 TCTTTTAGAA 0.841586 -181 TTAATAAAAATATTTTTATGCACGTAGTTGTG 2 161 0 TATTTTAGCA 0.965035 -103 CCTCAACTTGGATTTTGTTGCATATCTAAGAC 2 234 0 GATTTTTGCA 0.967808 -30 AATTCCTTTATATGCTGATGAACGGCTTGATA 3 102 0 TATGCTAGAA 0.814201 -132 CTCTACTCAAGATTTTCAATAAGCCTTCTACC 3 204 0 GATTTTATAA 0.780186 -30 ATACACCACTGATTTTTAAGCATCTTCAAGGT 4 23 0 GATTTTAGCA 0.977785 -228 GAATTAGAGAGATGTTTTTGAATGTTTTATGA 4 63 0 GATGTTTGAA 0.958138 -188 GTTTGAGAATTATATTATCGCATAAATAAAAA 5 59 0 TATATTTGCA 0.79649 -59 ATTCTCAAACGATGTTATAGAACAAGAATGTA 5 81 1 GATGTTTGAA 0.958138 -37 ****** * *** Masking position 6 Map Score: 6.73671 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 146 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 AGCAAAATGAAGAGTTCATAAGTCTTCCTGGG 2 10 0 AGAGTCTAAT 0.921981 -254 ATATTTTAACGAAGGTCATAATTGGTAGTGAGC 2 40 0 GAAGTCTAAT 0.921981 -224 CATTAAAAGAAGAGACGAAAACTTTTTTACATA 2 70 0 AGAGCGAAAT 0.8082 -194 TAGATTTTCTAAACTTCAAAAATGGAGATGTAA 2 116 0 AAACTCAAAT 0.964679 -148 ATCATTGTATAGAAGCCGAAAATATCATGATCG 2 202 1 AGAACCAAAT 0.847509 -62 AGCACTAGGAAAACCCCTAAAGTATCAAGCCGT 3 80 1 AAACCCAAAT 0.972347 -154 TAGTGTAAATGAACTTCATAATTTTATTACTAA 4 119 1 GAACTCTAAT 0.921981 -132 GTGGAAAATAGAAGATCCAAATTATAACAATTA 4 149 0 GAAGTCAAAT 0.957498 -102 GCCCTTATTTAAACACCAAAATTTTTATTTATG 5 38 1 AAACCCAAAT 0.972344 -80 **** ** *** * Masking position 10 Map Score: 4.27429 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 152 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 CTCCTTTATTTCCTTATCGAG 1 21 0 TCCTTTATTT 0.969319 -11 AAAGTTTTCGTCTCTTCTTTTAATGAAGCC 2 78 1 TCTCTTCTTT 0.963838 -186 CTCTTGTAATTCCTTTATATGCTGATGAAC 3 111 0 TCCTTTATAT 0.908955 -123 TATCCTCTTCCCCTTTCTATATGCCTCCTT 3 153 0 CCCTTTCTAT 0.879204 -81 TCTCTCTAATTCCCTTATTTTTTGAGATGT 4 83 1 TCCCTTATTT 0.976004 -168 ATAATTTGGATCTTCTATTTTCCACAAAGT 4 157 1 TCTTCTATTT 0.789787 -94 CTTTCTTCTCTCTTTTCTTTATTGCCCTTA 5 15 1 TCTTTTCTTT 0.953922 -103 TTTCTTTATTGCCCTTATTTAAACACCAAA 5 28 1 GCCCTTATTT 0.926011 -90 ATATCCTCTTCTTTTTTCAATTTT 6 5 1 CCTCTTCTTT 0.937861 -22 ********** Masking position 6 Map Score: 10.0035 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 293 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 GCTTCTATACAATGATAAACCTTCCTTAATA 2 187 0 AATGATAACC 0.983845 -77 GCTTATTGTTTCACCTTGAAGATGC 4 5 1 ATTGTTCACC 0.932754 -246 TTATGATCAAAATGATACACCACTGATTTTT 4 38 0 AATGATCACC 0.984751 -213 TATTTTTTGAGATGTTTAACCTAGTGTAAAT 4 98 1 GATGTTAACC 0.978291 -153 TATCAAGTCTGATGATGAACCTTCCCCTCAC 7 32 1 GATGATAACC 0.984989 -62 ****** **** Masking position 6 Map Score: 3.57411 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TTTAATGAAGCCTAGTAGTTTTACATCTCC 2 96 1 CCTAGTAGTT 0.931148 -168 GTGTAGGTAGCTTTGTAGATTTTCTAAACT 2 134 0 CTTTGTAGAT 0.916682 -130 ATCTCTCTTTCCTCGAGGATTTTAAGAATC 3 29 0 CCTCGAGGAT 0.926376 -205 TAGGGGTTTTCCTAGTGCTTGCCAAATTTC 3 69 0 CCTAGTGCTT 0.900512 -165 TATTGTTTCACCTTGAAGATGCTTAAAAAT 4 14 1 CCTTGAAGAT 0.946264 -237 AGATGTTTAACCTAGTGTAAATGAACTTCA 4 107 1 CCTAGTGTAA 0.768437 -144 TCTTGGTTCACTTTGTGGAAAATAGAAGAT 4 166 0 CTTTGTGGAA 0.864657 -85 ATTTGCCCCTCCTTGTACATTCTTGTTCTA 5 98 0 CCTTGTACAT 0.953046 -20 ********** Masking position 3 Map Score: 2.52481 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 351 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GGAAGAGGATATATTACAAGCTGACTGAGA 3 172 1 ATATTACAAG 0.923653 -62 AAGATCCAAATTATAACAATTAGTAATAAA 4 141 0 TTATAACAAT 0.925004 -110 ATCCAAAGAGATATAACCAGGCACCTCGCT 4 210 0 ATATAACCAG 0.947197 -41 AAACGATGTTATAGAACAAGAATGTACAAG 5 87 1 ATAGAACAAG 0.947147 -31 CTCTGAAAGTTTATAACAAT 7 1 0 TTATAACAAT 0.925004 -93 ********** Masking position 6 Map Score: 0.584329 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 29 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ACTACCAATTATGACCTTCGTTAAAATATGT 2 44 1 ATGACCTTCT 0.875651 -220 AAATATTTTTATGCACGTAGTTGTGTAGGTA 2 155 0 ATGCACGTAT 0.907417 -109 CGAAAATATCATGATCGTCTTAGATATGCAA 2 218 1 ATGATCGTCT 0.977763 -46 TTATATGCTGATGAACGGCTTGATACTTTAG 3 96 0 ATGAACGGCT 0.933382 -138 CCTAGTGTAAATGAACTTCATAATTTTATTA 4 117 1 ATGAACTTCT 0.615204 -134 ATATCCTCTTCTTTTTTCAATTT 6 3 1 ATCCTCTTCT 0.866369 -24 ********* * Masking position 2 Map Score: 0.289153 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 93 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ********** No masking Map Score: -1.88842e-14 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: -1.88842e-14 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: -1.88842e-14 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0